Stonar was originally established at Stour House in Sandwich which can be traced back as far as 1895.

In 1920 Stour House School was taken over by three joint heads Miss Gladys Crook, Miss Isabel Blackwell and Miss Edith Joslin, affectionately known by Stonarians as "the Three". They expanded the school to the extent that it outgrew its premises. The school was packed up and moved over the bridge to Stonar House "close to the sea, smoke-free air and spacious accommodation." From then on it became Stonar House School.

With its newly acquired extensive grounds, the first Stonar pony arrived – Tufty. By 1934 riding was firmly established at Stonar House.

Stonar House remained the school's home until 1939 and the outbreak of the Second World War, when the MOD requisitioned the land and the entire school community was forced to decamp. Luckily one of the Heads had relatives in Wiltshire who alerted her to Cottles Park. The school was packed up and moved to its current location. The School ponies, a goat called Ambrosia, a dog, a cat and a bowl of goldfish moved too. In the words of Miss Blackwell: "We were a tired and almost exhausted group of Stonarites who arrived late evening at our new domicile – Cottles Park – was it to be worth it in the future? The present Stonar School, Cottles Park must be the answer."

The "Three" continued to run Stonar until they retired in the 1960s. Their successor Miss Doreen Denmark expanded and developed the school for 20 years, until her retirement in the 1980s.

Since then Stonar and its unique Equestrian Centre have flourished with a committed staff, strong governance and excellent facilities within its superb parkland setting. Crucially, the school's pervading ethos from its earliest days, of warmth, support and a 'can do' attitude are as strong as ever.